{"id":"https://openalex.org/W2899837977","doi":"https://doi.org/10.1371/journal.pcbi.1006494","title":"Putting benchmarks in their rightful place: The heart of computational biology","display_name":"Putting benchmarks in their rightful place: The heart of computational biology","publication_year":2018,"publication_date":"2018-11-08","ids":{"openalex":"https://openalex.org/W2899837977","doi":"https://doi.org/10.1371/journal.pcbi.1006494","mag":"2899837977","pmid":"https://pubmed.ncbi.nlm.nih.gov/30408027"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006494","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006494","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006494&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"editorial","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006494&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023547268","display_name":"Bjoern Peters","orcid":"https://orcid.org/0000-0002-8457-6693"},"institutions":[{"id":"https://openalex.org/I1311191458","display_name":"La Jolla Institute for Immunology","ror":"https://ror.org/05vkpd318","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1311191458"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bjoern Peters","raw_affiliation_strings":["La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I1311191458"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046334676","display_name":"Steven E. Brenner","orcid":"https://orcid.org/0000-0001-7559-6185"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven E. Brenner","raw_affiliation_strings":["Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075157579","display_name":"Edwin Wang","orcid":"https://orcid.org/0000-0001-8689-5295"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Edwin Wang","raw_affiliation_strings":["Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada"],"affiliations":[{"raw_affiliation_string":"Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074883462","display_name":"Donna K. Slonim","orcid":"https://orcid.org/0000-0003-3357-437X"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Donna Slonim","raw_affiliation_strings":["Department of Computer Science and Genetics, Tufts University, Medford, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Genetics, Tufts University, Medford, Massachusetts, United States of America","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013292761","display_name":"Maricel G. Kann","orcid":"https://orcid.org/0000-0003-0116-3883"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maricel G. Kann","raw_affiliation_strings":["Department of Biological Sciences, University of Maryland, College Park, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Maryland, College Park, Maryland, United States of America","institution_ids":["https://openalex.org/I66946132"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5023547268"],"corresponding_institution_ids":["https://openalex.org/I1311191458"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.24919686,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.86941109,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"14","issue":"11","first_page":"e1006494","last_page":"e1006494"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9854000210762024,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9854000210762024,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9772999882698059,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9728999733924866,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7290410995483398},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.652717113494873},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.6403207182884216},{"id":"https://openalex.org/keywords/meaning","display_name":"Meaning (existential)","score":0.5632327198982239},{"id":"https://openalex.org/keywords/management-science","display_name":"Management science","score":0.390962153673172},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.20488294959068298},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11977684497833252}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7290410995483398},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.652717113494873},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.6403207182884216},{"id":"https://openalex.org/C2780876879","wikidata":"https://www.wikidata.org/wiki/Q3054749","display_name":"Meaning (existential)","level":2,"score":0.5632327198982239},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.390962153673172},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.20488294959068298},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11977684497833252},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1006494","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006494","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006494&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:30408027","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30408027","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1006494","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006494","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:eddcc878cd624c8096ba1e8ec6dc4395","is_oa":true,"landing_page_url":"https://doaj.org/article/eddcc878cd624c8096ba1e8ec6dc4395","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 14, Iss 11, p e1006494 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5202283","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6224028","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6224028","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6224028","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006494","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006494","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006494&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2899837977.pdf","grobid_xml":"https://content.openalex.org/works/W2899837977.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Research":[0],"in":[1,20,131],"computational":[2],"biology":[3],"has":[4,88],"given":[5],"rise":[6],"to":[7,14,33,35,70,104,108,127],"a":[8,27,37,45,76],"vast":[9],"number":[10],"of":[11,57,113,120],"methods":[12],"developed":[13],"solve":[15],"scientific":[16,38,96],"problems.":[17],"For":[18],"areas":[19],"which":[21,31,91],"many":[22],"approaches":[23,93],"exist,":[24],"researchers":[25],"have":[26],"hard":[28],"time":[29],"deciding":[30],"tool":[32],"select":[34],"address":[36],"challenge,":[39],"as":[40],"essentially":[41],"all":[42,53,56],"publications":[43],"introducing":[44],"new":[46,77,92],"method":[47],"will":[48],"claim":[49],"better":[50],"performance":[51,119],"than":[52],"others.":[54],"Not":[55],"these":[58],"claims":[59],"can":[60],"be":[61],"correct.":[62],"Equally,":[63],"for":[64,98],"this":[65,105],"same":[66],"reason,":[67],"developers":[68,126],"struggle":[69],"demonstrate":[71],"convincingly":[72],"that":[73,115],"they":[74],"created":[75],"and":[78,125],"superior":[79],"algorithm":[80],"or":[81],"implementation.":[82],"Moreover,":[83],"the":[84,99,118],"developer":[85],"community":[86],"often":[87],"difficulty":[89],"discerning":[90],"constitute":[94],"true":[95],"advances":[97],"field.":[100],"The":[101],"obvious":[102],"answer":[103],"conundrum":[106],"is":[107],"develop":[109],"benchmarks-meaning":[110],"standard":[111],"points":[112],"reference":[114],"facilitate":[116],"evaluating":[117],"different":[121],"tools-allowing":[122],"both":[123],"users":[124],"compare":[128],"multiple":[129],"tools":[130],"an":[132],"unbiased":[133],"fashion.":[134]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":4}],"updated_date":"2026-02-09T09:26:11.010843","created_date":"2025-10-10T00:00:00"}
